plotSpikeCI {CALIB} | R Documentation

## plot spike concentration vs measured intensity

### Description

plot spike known concentration and measured intensity of one array.

### Usage

    plotSpikeCI(spike, parameter,array = 1, bc = FALSE, area = TRUE,
                meanpoint = TRUE,xlab = "log(Concentration)",
                ylab = "log(Intensity)", main = colnames(spike$R)[array],
                onlycalib = TRUE, xlim = NULL, ylim = NULL, pch = 19,
                cex = 0.2, meanpch = 21, meancex = 1, lwd = 1.5,
                cy5col = "red", cy3col = "green", ...)

### Arguments

`spike` | a `SpikeList` object.
`parameter` | a `ParameterList` object.
`array` | integer giving the array to be plotted.
`bc` | a logical value. `TRUE` means background corrected measured intensities are used. Default is FALSE.
`area` | a logical value. `TRUE` means spot area is used to calculate measured intensities. Namly, measured intensities are calculated by foreground intensities(or background corrected intensities, if bc is `TRUE`) multiply spot area. `FALSE` means spot area is not used. Default is `TRUE`.
`meanpoint` | a logical value. `TRUE` is to show meanpoint of measured intensities with the same concentration on the plot. `FALSE` means not show.
`xlab` | a title for the x axis.
`ylab` | a title for the y axis.
`main` | an overall title for the plot.
`onlycalib` | a logical value. `TRUE` means only the calibration controls are on the plot. `FALSE` means to plot all the spikes
`xlim` | the x limits (min,max) of the plot.
`ylim` | the y limits of the plot.
`pch` | a integer code for one of plotting characters or symbols for the spike data set. Default is 21.
`cex` | a numerical value giving the amount by which the points which indicate spike data set should be scaled relative to the default. Default is 0.4.
`meanpch` | a integer code for one of plotting characters or symbols for the meanpoints. Default is 21.
`meancex` | a numerical value giving the amount by which the meanpoints should be scaled relative to the default value. Default is 1.
`lwd` | width of the model curves. Default is 1.5.
`cy5col` | color of all symbols for cy5. Default is red.
`cy3col` | color of all symbols for cy3. Default is green.
`...` | other graphical parameters can be used in function `plot`.

### Details

The function plots spike concentration and measured intensity of one array. array number is specified by the argument `array`. It accepts the concentration of given array from the agrument `spike`, which is a `SpikeList` object. The measured intensities are calculated from `spike`. Four different ways can be used to calculate the measured intensities. Arguments `bc` and `area` are logical and their combinations are used for specifying the four differents ways. `bc` indicates using background correction or not. `area` indicates multipling spot area or not. The default value of these two arguments are `bc` = FALSE and `area` = TRUE.

In order to help data visualization, meanpoints and model curve can be added on the plot. And the arguments `meanpoint` and `parameter` are correspond to these. The meadians of every group of measured intensities which have the same concentration are shown on the polt if `meanpoint` is true. Model curves of both dye are shown if the arguement `parameter` is specified after parameter estimation.

### Value

A plot is created on the current graphics device.

### Author(s)

Hui Zhao

### See Also

see graphic functions `plot`, `par`

### Examples

    # load data: spike
    data(spike)

    # specify the array to be plotted.
    array <- 1

    # use the default values for other parameters.
    plotSpikeCI(spike,array=array)

    # after parameter estimation, the model curves can be shown on the plot.
    data(parameter)
    plotSpikeCI(spike,parameter,array=array)

[Package CALIB version 1.10.0 Index]